Dear Troels, Are you aware of the caracas package for computer algebra in R? The package provides an interface to the SymPy package in python via the reticulate package.
I have no idea if the package can be helpful in your connection, but please report succeses and failures back. Best regards Søren -----Original Message----- From: Troels Ring <tr...@gvdnet.dk<mailto:troels%20ring%20%3ctr...@gvdnet.dk%3e>> To: Jeff Newmiller <jdnew...@dcn.davis.ca.us<mailto:jeff%20newmiller%20%3cjdnew...@dcn.davis.ca.us%3e>>, r-help@r-project.org<mailto:r-help@r-project.org>, "Ebert,Timothy Aaron" <teb...@ufl.edu<mailto:%22Ebert,timothy%20aaron%22%20%3cteb...@ufl.edu%3e>>, Valentin Petzel <valen...@petzel.at<mailto:valentin%20petzel%20%3cvalen...@petzel.at%3e>> Subject: Re: [R] R emulation of FindRoot in Mathematica Date: Thu, 19 Jan 2023 16:18:57 +0100 Hi Jeff - that is definitely not fair, this is a highly respected scientist but old me are probably not clever enough to explain problem which I think is not too difficult. Basically, it is a series of consecutive statements of H and Mg and K combining to ATP and ADP, creatin and creatinP under assumption og known total inorganic phosphate (pi), total ATP total ADP, creatin and creatinphosphate. It was written in 1997 when R was less mature - and if we know how to do it in R so not to depend on black box operations it would be fun. For the moment, I'm not even sure I understand why there is now focus on the problem being nonlinear, since I want to evaluate at given H or pH. hatp <- 10^6.494 * H * ATP ? BW Troels Den 19-01-2023 kl. 15:54 skrev Jeff Newmiller: But it is simultaneously an example of why some researchers like black box solvers... a system of dozens of nonlinear equations can potentially have many or even infinite solutions. If the researcher is weak in math, they may have no idea which solutions are possible and having a tool like FindRoot confidently return a solution lets them focus on other things. Sort of like ChatGPT. TL;DR the author may have no idea about how to resolve this without relying on the opaque FindRoot. On January 19, 2023 6:28:53 AM PST, "Ebert,Timothy Aaron" < <mailto:teb...@ufl.edu> teb...@ufl.edu > wrote: This is a poster child for why we like open source software. "I dump numbers into a black box and get numbers out but I cannot verify how the numbers out were calculated so they must be correct" approach to analysis does not really work for me. Tim -----Original Message----- From: R-help < <mailto:r-help-boun...@r-project.org> r-help-boun...@r-project.org > On Behalf Of Troels Ring Sent: Thursday, January 19, 2023 9:18 AM To: Valentin Petzel < <mailto:valen...@petzel.at> valen...@petzel.at >; r-help mailing list < <mailto:r-help@r-project.org> r-help@r-project.org > Subject: Re: [R] R emulation of FindRoot in Mathematica [External Email] Thanks, Valentin for the suggestion. I'm not sure I can go that way. I include below the statements from the paper containing the knowledge on the basis of which I would like to know at specified [H] the concentration of each of the many metabolites given the constraints. I have tried to contact the author to get the full code but it seems difficult. BW Troels hatp <- 10^6.494*H*atp hhatp <- 10^3.944*H*hatp hhhatp <- 10^1.9*H*hhatp hhhhatp <- 10*H*hhhatp mgatp <- 10^4.363*atp*mg mghatp <- 10^2.299*hatp*mg mg2atp <- 10^1-7*mg*mgatp katp <- 10^0.959*atp*k hadp <- 10^6.349*adp*H hhadp <- 10^3.819*hadp*H hhhadp <- 10*H*hhadp mgadp <- 10^3.294*mg*adp mghadp <- 10^1.61*mg*hadp mg2adp <- 10*mg*mgadp kadp <- 10^0.82*k*adp hpi <- 10^11.616*H*pi hhpi <- 10^6.7*h*hpi hhhpi <- 10^1.962*h*hhpi mgpi <- 10^3.4*mg*pi mghpi <- 10^1.946*mg*hpi mghhpi <- 10^1.19*mg*hhpi kpi <- 10^0.6*k*pi khpi <- 10^1.218*k*hpi khhpi <- 10^-0.2*k*hhpi hpcr <- 10^14.3*h*pcr hhpcr <- 10^4.5*h*hpcr hhhpcr <- 10^2.7*h*hhpcr hhhhpcr <- 100*h*hhhpcr mghpcr <- 10^1.6*mg*hpcr kpcr <- 10^0.74*k*pcr khpcr <- 10^0.31*k*hpcr khhpcr <- 10^-0.13*k*hhpcr hcr <- 10^14.3*h*cr hhcr <- 10^2.512*h*hcr hlactate <- 10^3.66*h*lactate mglactate <- 10^0.93*mg*lactate tatp <- atp + hatp + hhatp + hhhatp + mgatp + mghatp + mg2atp + katp tadp <- adp + hadp + hhadp + hhhadp + mghadp + mgadp + mg2adp + kadp tpi <- pi + hpi + hhpi + hhhpi + mgpi + mghpi + mghhpi + kpi + khpi + khhpi tpcr <- pcr + hpcr + hhpcr + hhhpcr + hhhhpcr + mghpcr + kpcr + khpcr + khhpcr tcr <- cr + hcr + hhcr tmg <- mg + mgatp + mghatp + mg2atp + mgadp + mghadp + mg2adp + mgpi + kghpi + mghhpi + mghpcr + mglactate tk <- k + katp + kadp + kpi + khpi + khhpi + kpcr + khpcr + khhpcr tlactate <- lactate + hlactate + mglactate # conditions tatp <- 0.008 tpcr <- 0.042 tcr <- 0.004 tadp <- 0.00001 tpi <- 0.003 tlactate <- 0.005 # free K and Mg constrained to be fixed # mg <- 0.0006 k <- 0.12 Den 19-01-2023 kl. 12:11 skrev Valentin Petzel: Hello Troels, As fair as I understand you attempt to numerically solve a system of non linear equations in multiple variables in R. R does not provide this functionality natively, but have you tried multiroot from the rootSolve package: <https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fcran> https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fcran .r-project.org%2Fweb%2Fpackages%2FrootSolve%2FrootSolve.pdf&data=05%7C 01%7Ctebert%40ufl.edu%7C7cb98cd926b34284cd5f08dafa28026c%7C0d4da0f84a3 14d76ace60a62331e1b84%7C0%7C0%7C638097347110882622%7CUnknown%7CTWFpbGZ sb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3 D%7C3000%7C%7C%7C&sdata=D9A3fwJ5x7GbEV4A01wncLUil7szTdSPul5vd0lsSBw%3D &reserved=0 multiroot is called like multiroot(f, start, ...) where f is a function of one argument which is a vector of n values (representing the n variables) and returning a vector of d values (symbolising the d equations) and start is a vector of length n. E.g. if we want so solve x^2 + y^2 + z^2 = 1 x^3-y^3 = 0 x - z = 0 (which is of course equivalent to x = y = z, x^2 + y^2 + z^2 = 1, so x = y = z = ±sqrt(1/3) ~ 0.577) we'd enter f <- function(x) c(x[1]**2 + x[2]**2 + x[3]**2 - 1, x[1]**3 - x[2]**3, x[1] - x[3]) multiroot(f, c(0,0,0)) which yields $root [1] 0.5773502 0.5773505 0.5773502 $f.root [1] 1.412261e-07 -2.197939e-07 0.000000e+00 $iter [1] 31 $estim.precis [1] 1.2034e-07 Best regards, Valentin Am Donnerstag, 19. Jänner 2023, 10:41:22 CET schrieb Troels Ring: Hi friends - I hope this is not a misplaced question. From the literature (Kushmerick AJP 1997;272:C1739-C1747) I have a series of Mathematica equations which are solved together to yield over different pH values the concentrations of metabolites in skeletal muscle using the Mathematica function FindRoot((E1,E2...),(V2,V2..)] where E is a list of equations and V list of variables. Most of the equations are individual binding reactions of the form 10^6.494*atp*h == hatp and next 10^9.944*hatp*h ==hhatp describing binding of singe protons or Mg or K to ATP or creatin for example, but we also have constraints giving total concentrations of say ATP i.e. ATP + ATPH, ATPH2..ATP.Mg I have, without success, tried to find ways to do this in R - I have 36 equations on 36 variables and 8 equations on total concentrations. As far as I can see from the definition of FindRoot in Wolfram, Newton search or secant search is employed. I'm on Windows R 4.2.2 Best wishes Troels Ring, MD Aalborg, Denmark ______________________________________________ <mailto:R-help@r-project.org> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see <https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fst> https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fst at.ethz.ch%2Fmailman%2Flistinfo%2Fr-help&data=05%7C01%7Ctebert%40ufl .edu%7C7cb98cd926b34284cd5f08dafa28026c%7C0d4da0f84a314d76ace60a6233 1e1b84%7C0%7C0%7C638097347110882622%7CUnknown%7CTWFpbGZsb3d8eyJWIjoi MC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C %7C%7C&sdata=7DTBQItdQpAqK%2FCS1%2BqQvYdlvjyJMjzTOXhoS6AY%2FJQ%3D&re served=0 PLEASE do read the posting guide <https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.r> https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.r -project.org%2Fposting-guide.html&data=05%7C01%7Ctebert%40ufl.edu%7C7c b98cd926b34284cd5f08dafa28026c%7C0d4da0f84a314d76ace60a62331e1b84%7C0% 7C0%7C638097347110882622%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiL CJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=m0 0vZP75nk9icL6H8Gc0dH1bHhkRCS9I5N27uORQmQ0%3D&reserved=0 and provide commented, minimal, self-contained, reproducible code. 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